First question I would ask the witnesses is when and where have you heard a missle fly over your head. I bet that not one person there could say that they have heard a missle. As for the sound, if you listen to the sound of the planes that hit the trade centers, you will notice that the engines are firewalled. That would explain the loud whoosh noise as the airplane went overhead.
These airliners were flown at such a high speed so the military won't have enough time to intercept them and shoot them down. When an ailiner hits the ground while traveling at over 400 MPH, there tends to be nothing left of the aircraft because it desentigrates. The poeple inside the airliner desintigrate as well. If you study the video of one of the planes that struck the towers, you will see that the cockpit actually comes through the other side of the building intact, and then turns into dust almost immediately. I have studied the tapes and this is what I see.
In the linked video, it shows that an aircraft that crashes leaves debris. Not one of those crashes shown were of airliners that hit the ground at over 400 MPh. All that would have been left at the pentagon and trade centers would have been small pieces and engines. The engines would have made it deep into the pentagon.